But human flesh was too frail, too paltry to hold the terrific essence that was Khosatral Khel. So he stood up in the shape and aspect of a man, but his flesh was not flesh; nor the bone, bone; nor blood, blood. He became a blasphemy against all nature, for he caused to live and think and act a basic substance that before had never known the pulse and stir of animate being.
In Haruhi Suzumiya, Kuyou Suou / Suou Kuyou (the proper order is purposefully left unknown). While the other Humanoid Interfaces are weird, Kuyou is described by the narration as simply wrong. Her ordinary movements like walking seem to defy the laws of physics in inexplicable ways, and her words and motivations are even less comprehensible than the others. Kyon is terrified to simply be in her presence.
In Soul Eater, many of the Great Old Ones take humanoid shapes but are regarded as something inhuman and spiritually beyond the realms of human comprehension. The primary example is probably Asura, the incarnation of madness, whose presence causes hallucinations and reality to go wibbly-wobbly. Lord Death is a more benign example.
Father looks like a normal middle aged man. Anything else would be a massive spoiler, but let's just say he's not.
Most of the Homunculi can easily pass for human, but their true forms show them to be almost as nasty as Father. Special mention goes to Pride (a colossal shadowy mass of tentacles, eyes, and teeth) and Gluttony (a "fake" Gate of Truth).
In Apocalypse no Toride (Fortress of The Apocalypse) the four juvenile delinquents escape from prison (which has been overrun with zombies) into the city and encounter a giant mountain of rotting zombies controlled by an androgynous naked man on the top, using the zombies like a grotesque throne. When Maeda catches its attention, said naked man (who was about a half-mile away) uses the zombies to move like a hideous organism at lightning speed, until it's only a foot in front of the terrified youth. A close-up reveals that it has Sharingan-like eyes, with three smaller eyes inhabiting each of its pupils.
Neon Genesis Evangelion has Rei and Kaworu, who are the soul (or part of a soul) of an Angel jammed into a soulless clone body, and are even more powerful and just as incomprehensible as the "regular" Angels.
Baccano! has Ronnie Schiatto, an ancient and incomprehensibly powerful "demon" who decided to take human form and become a gangster for the lulz. While he's usually content to just sit back and be the All-Powerful Bystander, sometimes he likes to switch his Lovecraftian terror aura on while still in human form - it does wonders for negotiations.
If he had just been a simple mafioso, those gathered there would not have felt such an alien sense of awe. The aura rolling off of him was that of innumerable things mixed chaotically together... of something that was not human.
Gessho Kuki, aka The Shadow, and Big Bad of Kagerou-Nostalgia may look like a man (albeit one who is deep into the Uncanny Valley) but is not, and never was, human. He's eventually revealed as a mass of evil magic left behind by previous Big Bad King Haku, and trapped in the form of a man. When he loses his temper he goes One-Winged Angel, changing into a billowing mass of magic that keeps only his human form's eyes.
Claymore has AwakenedPriscilla, a nightmare that makes other nightmares crap their pants and required a different Abomination to perform a Fusion Dance to gain even a chance of defeating her, yet most of the time looks like a very spiky human woman. Her power so vastly outclasses the other Awakened Beings that she has been called a Physical God.
Doctor Manhattan of Watchmen fame shows signs of becoming this throughout the story due to his growing detachment from, well, everything. He ultimately embraces humanity, sort of, but not his own. At best you could say he recognizes the value of humanity. What he actually does is to go off to a galaxy far, far away to play God.
The Shade looks and acts human enough (though some artists do portray him with a certain pallor), but his powers are taken straight from the fabric of a dimension holding a godlike Eldritch Abomination and have essentially become one with him, making him ageless and virtually unkillable, not to mention terrifyingly powerful. Thankfully for us, he's generally a fairly nice guy (not a hero by any means, but definitely not an outright villain either) and is perfectly willing to leave you be... that is, unless you attempt to attack Opal City. In that case, all bets are off.
Golden Age public domain superhero Stardust The Super Wizard is an unintentional one. Imagine a character with the reality-warping power of Dr. Manhattan as mentioned above combined with the black and white worldview and the "creative" mind of his "colleague" Rorschach and you have Stardust.
Why he's like this is likely because his creator, Fletcher Hanks, was by all accounts a terrible person, and the combination of Hanks' warped worldview with said Reality Warper powers makes the character both this trope, and also disturbing to read in the same way as a serial killer's diary.
Mad Jim Jaspers of Captain Britain crosses into this realm thanks to his abilities being strong enough to make him nigh-omnipotent, with it being heavily implied that he exists partially in a metaphysical realm, as well. He's so powerful that his entire continuity had to be destroyed to prevent it from becoming infectious and warping reality in other continuities. Earth-616 also has Jaspers, and he's even more powerful. It took an invincible, infinitely adaptable killing machine that the original Jaspers created and that escaped from the destroyed continuity to bring the 616 Jaspers down. It transported him to a reality-free area to deprive him of fuel for his abilities. The resulting toll on the being was so great that he was put down without much difficulty by Captain UK.
The Moonchild/Antichrist from The League of Extraordinary Gentlemen is a bald man that can grow into gigantic heights with eyes all over his body. He progressively looks worse as the heroes try to hack him apart, rendering him a fleshy pile that quickly regenerates into his original form. He also happens to be Harry Potter.
Abraxas looks like a human with green skin who wears a toga, and he makes Galactus seem positively cuddly in comparison. Indeed, one of the reasons Galactus even exists is to keep Abraxas in check. Abraxas is the opposite of Eternity, making Abraxas the ultimate embodiment of unfettered destruction in the Marvel multiverse. Abraxas is fully willing and capable of killing entire universes, and the only way to get rid of him other than by reviving Galactus is to destroy all reality.
Psyko, the warped Evil Counterpart to Sleepwalker, was originally human before he was exposed to a wave of perverted demonic energy from the Mindscape. It completely fried the brains of every other human in the area, but he simply absorbed it and turned into a humanoid... thing with bone-white skin, a skull-like face, bone-like spikes growing out of his body, insane glowing eyes, and teeth as long as a man's finger.
Yuuka Kazami in the Touhou fanfiction Imperfect Metamorphosis is horrifically powerful, inspires petrifying dread by her very presence, not even Yukari knows what the hell she is (and notes that her powers are disturbingly ineffective against her), and even with the Shadow Youkai running around and causing a mess of everything nearly everyone treats her as the bigger threat. Later events reveal she's actually an Outer God, straight out of Lovecraft.
Naruto/Sunny in Dancing With Demons is either this or past the Bishounen Line depending on who's dealing with him. Most women and many children find his hair ornaments, flawless skin, and blonde hair "beautiful". Most ninja find his red eyes, unnatural stillness, and carnivorous diet (humans if he can manage it) highly disturbing.
Played with relentlessly in Only Human, a Star Trek: The Next Generation AU where Q never regained his powers in "Deja Qu". Q makes a poor human and it becomes clear that Q's powers were simply advanced technology and his reasoning is comprehensible by humans if they know where he's coming from. Except Q is still an alien in human form and his prior existence is still so alien it is only expressible by analogy. His expectations and reactions don't make sense without that history.
The "Mystery Man" in Lost Highway, while his true morals or intention is open to interpretation, can certainly come off as this to a first time viewer. The extensive make-up that covers his eyebrows and makes him inhumanly pale and the camera's tendency to get uncomfortably close to his face during his scenes certainly doesn't help.
From the Phantasm franchise, The Tall Man is perhaps one of the best known examples of this on film. He looks like an old man in a suit, albeit an intimidating one, but is really implied to be some horrible otherdimensional conciousness wearing the form of a man named Jebadaiah Morningstar like a meat suit. He bleeds a yellowish fluid when injured and his fingers have been known to turn into hideous bug-things when severed. He is hideously strong, controls an army of deadly silver spheres, and even has some Reality Warper powers. He has a nasty agenda that involves killing people and turning them into twisted dwarfish slaves to use in another dimension.
"Everyone who saw her at the police court said she was at once the most beautiful woman and the most repulsive they had ever set eyes on. I have spoken to a man who saw her, and I assure you he positively shuddered as he tried to describe the woman, but he couldn't tell why."
According to the Star Wars Expanded Universe, Darth Sidious (Emperor Palpatine) developed into one of these. He was already one of the most powerful Force users of all time and is believed to have mastered all known Force abilities and invented new ones. He could do things like feed off the life essences of billions and create Force Storms, wherein he would rip open the time-space continuum with his sheer will alone and create a hyperspace wormhole capable of killing an entire world. He was even strong enough to cloud the vision of the entire Jedi Order. By the time of his final death in Dark Empire he had become a nexus of the Dark Side itself and was tearing holes in reality with his very existence.
In The Light Fantastic, everyone expects the Things From The Dungeon Dimensions to come storming into our reality with tentacles waving, but all they need is one mind. And when Rincewind looks into Trymon's eyes, it's every bit as horrific as anything involving tentacles and Alien Geometries.
I Shall Wear Midnight introduces the Cunning Man, the shade of a fanatic witch-hunter who was so obsessed he went on even after eventually having no body. He appears as a man in black with empty holes for eyes (no, not empty eye sockets, HOLES, you can see through them) and Invisible to Normals; to those who can perceive it, he also appears to exude a terrible stench, though rather than an actual physical stench this is their mind's perception of the corruption in his. He can use mirrors, pictures and the like to enter the world, and can possess the bodies of others. To hammer home how utterly wrong he is, it should be noted that, in Discworld, the eyes always show a person's true nature. Even the gods can change anything about their appearance except their eyes. Now the Cunning Man has nothing there, as in seeing into the front and out the back of his head.
The Beast, AKA Martin Chatwin from The Magicians is mistaken for an Eldritch Abomination at first, but during the climactic battle, his Evil Gloating reveals that, as a boy, he escaped into the fringes of the Fillory world and accepted the darker magic of its inhabitants wholeheartedly, transforming him into a god-level power. The result is not pretty◊
Cassandra, the antagonist of Full Tilt, appears as a young woman with red hair and blue eyes. It's made apparent almost immediately that she's very old and very powerful, and that she created the supernaturalAmusement Park of Doom in which most of the story is spent. However, she tends to either influence things from a distance, or get involved through use of weaponry rather than magic—her only direct demonstration of her true nature is a Stealth Hi/Bye.
The Shrike in Dan Simmons' Hyperion Cantos is a ten foot tall, four armed razor covered thing that can manipulate time and indiscriminately kills anyone who gets too near the "Time Tombs" on the titular planet.
The Clockmaker, from Alastair Reynolds' The Prefect. Can assume any shape, but its default form resembles a stretched out human form, spindly and quicksilver. Enjoys wanton slaughter and leaving intricately designed clocks and trinkets around... which may or may not be Body Horror-inducing booby traps.
Angleton, AKA the Eater of Souls in Charles Stross' The Laundry Series is eventually revealed to be this. Subverted in that he's undeniably one of the good guys, even if he lives in the Uncanny Valley and therefore frightens the hell out of his subordinates. What happened was that he was summoned and bound in the 1930s, taught to pass for human, and eventually Humanity Ensues. Strangely, it's implied that he believes in decency and fairness more than the people around him—he's not averse to pulling a few strings for Bob and Mo's sake.
All over the place in The Dresden Files. There's the two Faerie Queens, Mab and Titania, who are unfathomable even by fae standards and the Lords of the Outer Night in the Red Court. Then there are the Faerie "mothers", who are an order of magnitude more powerful than the queens. Some Outsiders can also take humanoid form, such as "Sharkface" in Cold Days.
The Myrddraal from the The Wheel of Time are comparatively minor examples, but they still qualify. Born among the Trollocs, they're a throwback to the Trollocs' human heritage, but warped by the Black Magic that created them- they resemble eerily pale, graceful humans except that they have smooth skin where eyes should be and have a number of bizarre abilities that cannot be explained by the series' main magic system. They're also absolutely devoid of emotion except for cold-blooded sadism and are all completely identical in terms of appearance and personality. Even human villains who encounter them are prone to remark on how unnatural they are.
And there is Shaidar Haran, a Myrddraal that acts as the Dark One's avatar, and later an incubator of sorts.
And Padan Fain, who starts out as human, but through a convuluted series of misfortunes, becomes the living embodiment of another evil power, possibly as bad as the Dark One.
Most of the plot in Graeme Penman's Motherland revolves around the villain trying very hard to become a Humanoid Abomination as opposed to the malevolent cloud that he is at the moment.
"I suppose you could call them men, yes. Two legs, two arms, a head each."
The Endlords from Sword of Shadows look like tall humans in dark armor, but it's made quite plain that they are in fact cosmic forces of destruction which have been compressed into this shape, and are utterly inimical to life as we know it.
Illyria's original form was a massive tentacled creature; she's an Old One, a shout-out to H. P. Lovecraft. But since she's stolen Winifred Burkle's body, we mostly see her looking like a blue version of Fred.
Jasmine. The most we could get from her true form was a shadowed mass of tentacles, and she s mentioned by her abandoned demon followers as the "Blessed Devourer." Those who are immune to her mind-control charms don't see her as a beautiful woman but a corpse filled with maggots, and her true name cannot be pronounced by human words (Angel needed a stitched up demon follower because it was the only thing capable of saying her name and breaking the spell).
Buffy the Vampire Slayer had one of these as its Season Five Big Bad. Glorificus, aka Glory, was an exiled hellgod that was reduced to using a hapless human host as a timeshare. Whenever Glory takes control of its (male) host, it looks like a glamorous woman. Even in this form Glory is a Nigh Invulnerablesuperstrong menace that can rob people of their sanity and eat it.
The Time Lords at the end of the Second War in Heaven and the Last Great Time War have continued to regenerate into forms that are ideal for waging chronological war - in the first case, war against what can only be approximately described as a sapient timeline. Guess what this implies for ordinary Time Lords?
Consider this description of the being the Pandorica was designed to hold: "A nameless, terrible thing, soaked in the blood of a billion galaxies. The most feared being in all the cosmos. And nothing could stop it, or hold it, or reason with it. One day it would just drop out of the sky and tear down your world." It's the Doctor.
In "The Family of Blood", when "John Smith", the Doctor's temporarily human persona, is told of his true identity and given a description of what the Doctor is like, it completely scares the hell out of him;
Tim Latimer: He's like fire and ice and rage. He's like the night and the storm in the heart of the sun...
"John Smith": *Quietly* Stop it.
Tim Latimer: He's ancient and forever. He burns at the centre of time and can see the turn of the universe...
"John Smith": *Panicking* Stop it, I said stop it!
The Celestial Toymaker, in the original series serial of the same name, resembles a middle-aged Caucasian man dressed in Mandarin robes who engages in silly, over-sized versions of board games and toys. He however controls his own universe and has vast powers over time and space. In one Expanded Universe novel, he is depicted more horribly and is outright stated to be using the powers of the Great Old Ones.
Also in the Expanded Universe, humanoid TARDISes... it's mentioned as being especially creepy when they open to take on passengers.
BOB from Twin Peaks is this—Humanoid on the outside, Abomination within.
LOST gives us the Man in Black, a post-human entity who takes the appearance of deceased individuals when not being a cloud of black smoke.
Kenneth in 30 Rock. Oddly, he combines this with being The Pollyanna. See his first words, said the day he was born.
Momma, I am not a person. My body's just a flesh vessel for an immortal being whose name, if you heard it, you would lose your mind.
A lot of creatures in Supernatural hijack human bodies because their real forms are incorporeal, but the Angels are the only ones who qualify for this trope. Their celestial forms are decidedly of the Eldritchy variety, completely incomprehensible to humans, and variously described as "multi-dimensional wavelengths of celestial intent" and the size of the Chrysler building. Whenever they appear in their true forms, all that is seen is a blinding light that engulfs the entire area, a booming deafening sound that are apparently their voices, everything in the vicinity getting destroyed due to their awesome presence, and are so much of a Brown Note that any humans nearby have their eyes burn out of their sockets and die. To manifest on Earth they use human vessels, which are purely intended as A Form You Are Comfortable With.
In Luca Turilli's Prophet of the Last Eclipse this seems to be the case with those touched by the Black Portal. They appear perfectly human, but demons (which can literally never die and may very well be true abominations in their own right) are instinctively terrified of them. And spilling the blood of one can result in The End of the World as We Know It.
Imaginos, the central figure of the Blue Öyster Cult album of the same name, is most definitely this. Admittedly, prior to being 'recruited' by Les Invisibles he was more 'humanoid' since he apparently thought of himself as human despite being a psychic shapeshifter, but afterwards he became more of a 'abomination' and is downright gleeful about it.
Marilyn Manson's concept album Antichrist Superstar has, well, the Antichrist Superstar, the reality-destroying result of The Worm becoming fed up with his sycophantic followers. While his appearance was unknown, the finished-but-unreleased video for Antichrist Superstar was leaked almost a decade later, which does show him in this form. If the Grim Reaper had sex with a fallen angel and they somehow had a kid, it would be an apt description.
The Boogieman from [[Gorillaz]] is a humanoid creature with a gas mask and a skeletal body beneath his cloak.
The Evangelist qualifies for this as well,although she is much more benevolent towards humans.
Mythology and Religion
If you look at urban myth, The Grinning Man, the Moth Man, Springheeled Jack, the Cornish Owlman, La Llorona, Black-Eyed Kids, heck, quite a lot of urban myths or cryptid sightings run on this trope. Many of these things might actually result from encounters with owls, specially barn owls, which they frequently resemble with the massive eyes and wing-like arms. Owls themselves, much like some other birds, do look vaguely humanoid, being erect bipeds, which is part of why they're frequently considered unnerving.
Nyx, personification of Night from Classical Mythology. Usually represented as a beautiful female human, yet a quick look at her children - most of which she gave birth to by herself alone - should tell you what kind of being she really is. If that doesn't convince you yet, the fact that even Zeusfears her should.
Also from Classical Mythology are the Gorgons - Stheno, Euryale, and Medusa. They have snakes for hair and long fangs, but it's the fact that looking at them will turn you to stone that really should serve as a red flag.
Cú Chulainn, the young hero of the Ulster Cycle of Celtic Mythology, particularly of the Táin Bó Cúailnge. Though he is portrayed as being as Bishōnen as a teenaged Irish ginger can be, he is a descendant from the Fomorians, a monstrous race from the mythic prehistory era of Ireland. Though he is heroic and stalwart, and generally perceived as a good guy, his defining mystical characteristic is his ability to transform into various disfigured superpowered abominations through the use of his warp-spasm. After he transforms, he becomes a berserker that slaughters anything in his path, friend and foe alike.
Some of the angels in Abrahamic religions, such as Christianity and Judaism. It is clear that some angels like Gabriel can appear as humanoid, but their real forms are at best highly confusing and at worst mind-numbingly horrifying. And they're not even alive anyway, as their entry on Eldritch Abomination shows. Note that only some bother to appear as humanoid however, as many in The Bible and The Qur'an don't even bother to disguise their real forms.
Daniel saw an angel that was invisible to everyone else, carried with it an aura of fear, and had a glowing face (like lightning) and eyes of flame. Also a body carved from gemstones.
According to one interpretation, a lot of the angels mentioned early on in the Bible (especially in B'reshit/Genesis) are in essence the will of God made manifest in temporary human form. So while they're described as men in the text, they really really aren't.
Satan is described as "appearing in the guise of a young man."
The angel of the lord itself is described as a man who was "terrifying to look at" by Samson's mother and when Samson's father asked its name he replied "You wouldn't understand if I told you." Despite or perhaps because of this, apocryphal works call him Metatron which basically means "less than four the letter word" (Tetragrammaton, a title for God).
It may be worth noting that that favorite adjective of Lovecraft, 'eldritch,' was originally a version of 'elven' . . .
Atropals from Epic-level DnD, the stillborn fetuses of Gods, also capable of shedding smaller Atropal Scions. Unsurprisingly, they are as terrifying, powerful and hideous as the description suggests.
Daelkyr from Eberron, high-level outsiders from the plane of madness. Notable in that they looked like this when they invaded the main continent ages prior, before humans had ever set foot there. When human explorers did arrive, later, they created a panic among the demihuman populace due to the resemblance. Keith Baker, creator of Eberron, was once asked why daelkyr looked so much like humans. His response was that the real question is why do humans look so much like daelkyr...
The Lady of Pain from the Planescape setting. Beyond her vaguely humanoid appearance (a ten foot floating humanoid in a robe with no visible feet and a frozen female face surrounded by a crown of blades), nobody knows anything about what or who she is, save that anyone who disrupts Sigil's day-to-day life or directly interacts with her in any way tend to get Flayed Alive on the spot. Inside of Sigil she is essentially omnipotent and not even gods can set foot there if she doesn't want them there.
Mage: The Awakening has "the Other," the Astral Aeon of the Abyss, who is said to look simply like an unassuming, shrunken, slightly odd old man, who nevertheless has something indescribably off with everything about him.
Similarly, each of the True Fae from Changeling: The Lost has a humanoid Mask that they can wear when they appear on Earth. These masks can be beautiful or hideous, but usually within the realm of human expectation... except for the one element that's just wrong.
This is also what most mages think of geniuses — that they are bizarre cosmic intelligences of unknown motivation and origins who simply look human. In the case of the Illuminated, they may well be right. The "inverted Geniuses" known as Clockstoppers may also be examples — one of the most powerful is described as being more a force of nature than a man.
Old World of Darkness has the Onceborn of Wraith: The Oblivion, effectively dead gods in service of the necrotic force known as Oblivion. Unlike their cohorts, the Neverborn, they were human at one point... but they were such bastards in life, they plummeted right into becoming Spectres upon death, and then ascended to the ranks of horrible divinity.
The Yozis and their varioussouls can appear in any number of bizarre, logic-defying forms, including entire living worlds... or they can appear as inhumanly attractive humanoid beings with a few thematic characteristics here and there. They can also do both at the same time — all demons above the First Circle have the ability to manifest in multiple locations at once. The Primordials Gaia and Autochthon are just as eldritch, except they haven't been mutilated and imprisoned in Hell. Gaia's most familiar form is a beautiful humanoid goddess who hangs out in Heaven.
The Fair Folk qualify, being even more monstrous and alien in this setting than is standard for that trope — they come from what is essentially an alien universe characterized by having no laws of physics, they have no actual personalities or motives, and they can only exist in Creation by eating human souls. Yet, as far as appearance goes, many of the Raksha nobles are inhuman only in their extreme beauty. It helps attract prey, you see.
According to Word of Sol, the Green Sun Princes qualify to a degree, having taken the Yozi nature into their once-human souls, and are gradually evolving into Yozi-like beings.
In a way, all of the Exalted are this. Human beings were never meant to receive power in the manner of the Exalted, and elder Exalts tend to have viewpoints that are rather skewed for one reason or another. They can also easily be impossibly beautiful.
The Immortal God Emperor of Mankind. Long ago, all of Earth's mages, psykers, and mystics decided that humanity needed a champion to lead them. They committed mass suicide and all of them were reincarnated as one being: the Emperor. Anyone who had the misfortune to make psychic contact with him and got a glimpse of what lay beneath the surface, such as John Grammaticus (a powerful psyker in his own right), would be left in a state of total awe and terror — mostly terror. The making of Astropaths even uses this deliberately, the aspiring Astropath making contact with the (severely weakened, maybe dead) Emperor for a brief instant, with the delightful effect of being able to transmit signals across the galaxy as well as having their eyes burned from their sockets.
Horus became one of these at the end of the Horus Heresy, with all four of the Chaos gods using him as a vessel of their power at once. The battle between him and the Emperor left him dead and the Emperor mortally wounded.
Over in Chuubo's Marvelous Wish-Granting Engine, there's the Best Friend and Billy Sovereign, who have ties to the Actuals of Nobilis. Billy is a pure example, but the Best Friend has actually gained a soul, which the Actuals are usually incapable of doing. Chuubo's also has Excrucians, under the name Riders, but they don't have as much world-ending horrible doom power, and all of them are at least to a degree playable out of the corebook.
Agonistes from the Tortured Souls line, who appears as a tall, powerfully-built man dressed in black leather and chains, his face horribly scarred and mutilated into a permanent Slasher Smile (if that sounds familiar, it should - the toy line was created by Clive Barker). Hand-made by an insane God on the seventh day of Creation, he answers the prayers of those who seek revenge on their enemies, remaking their bodies and transforming them into living weapons. While he isn't malicious (he only transforms people who come to him willingly), he's still beyond human morality - all he cares about is the "art" he can create with his supplicants.
Most Final FantasyBig Bads pass through this at some stage of their life cycle. They almost all pass out of it later when powering up, advancing to more conventional abominations, of course, but the intermediate stages still qualify.
Exdeath is actually an aggregate of evil souls trapped in a tree, but spends most of the game as a humanoid suit of armor. How he managed to fit a classic Eldritch Abomination appearance like his into a suit of armor small and human enough to deceive people isn't known, but he isa wizard.
Ultimecia managed to destroy time itself but still exists quite comfortably and is a Sorceress, something not quite human but looking the same, until the final boss fight; she loses the "humanoid" part when she shifts from "break the universe" mode into "break the skulls of the impudent mortals before me" mode.
Yu Yevon was once human, but turned into a jellyfish-summon-disease-thing using the only powers available to him as a human and instead simply wears an actual Eldritch Abomination as a suit of armour. He counted back in the day when he made the first Sin, though, and might have counted longer depending. We don't really know the how or why of his current blobby appearance, so it might have been a gradual thing.
Vayne Solidor started out as an ordinary Hume, albeit one who knew kung fu. Then the godlike Occuria Venat, out of gratitude for Vayne's help in fulfilling her Evil Plan, merged with him so that he would not face death alone. This fusion became The Undying, a humanoid monstrosity with pieces of Vayne's sky fortress attached to it that gave it the appearance of a mecha-angel.
Organization XIII from Kingdom Hearts II. Like the rest of their Nobody brethren, their semi-existence is so unnatural, so deeply wrong that even the darkness rejects them. Unlike the others, however, they look exactly like humans with odd powers. And oddly enough, being a Nobody is only a temporary affliction.
On that note, most Nobodies resemble humans in shape. All they are in reality are stretchy rag dolls who apparently have taken combat lessons from Voldo.
Special mention goes to Xion for not actually being a Nobody. That's right, even the Nobodies rejected her.
The prequel has Vanitas, a being made from another character's Darkness and is the original Unversed and origin of every Unversed you fight in the game.
Persona has Nyarlatothep taking the form of Jun's father in Innocent Sin, and of Tatsuya himself in Eternal Punishment.
In Persona 3, the Death Arcana itself is revealed to have somewhat unwittingly taken on a human form: firstly the Creepy Child Pharos, who then transforms himself and unknowingly becomes your new classmate Ryoji Mochizuki.
In Persona 4, one of these is an ally and eventual party member: Teddy is a Shadow whose desire for forming friendships with humans causes him to appear as a cartoony bear costume, which is empty inside. Eventually after becoming a party member, he crosses over to the real world and literally grows an entire human body for his essence inside of his costume so he can interact with people.
In the Shin Megami Tensei series, Alice, the recurring Elegant Gothic Lolita, who looks so human she has been often mistaken for an innocent, normal girl. She's actually something far worse than the series' standard Fiends and Undead. In Devil Survivor 2, her Racial Skill is Unearthly Form.
ADOM has several. Certainly there's Nuurag-Vaarn, the Chaos Archmage, who is the penultimate Boss Fight for the normal ending. He appears as a withered old man whose eyes are holes radiating such unbearable light of power you can barely catch a glimpse of the tentacles writhing in them. (Well, actually he appears as a "@" but this is what the description says.)
Heretic: Aside from the fact that we never see his face, or body for that matter, there's nothing visibly inhuman about D'Sparil's appearance, even though he's a demon that slipped in through a hole in the walls of the cosmos from the outside. He makes up for this by riding a humanoid serpent with an appropriately eldritch appearance.
The Heresiarch from Hexen, a near-unique boss creature, is an immensely powerful magic-using humanoid creature of some sort. Most of its appearance is hidden inside its robes, like D'Sparil's, but claws and a tail can be seen at the bottom. It's a leader of the cult of the Serpent Riders, but there isn't really much of an indication what it actually is, aside from something eldritch and unnatural.
Lavos from Chrono Trigger. At its core, beyond all its protective layers, it resembles nothing more than a (comparatively) small humanoid alien astronaut. That is also its most hideously powerful form, whose mere presences distorts time and space. And it's not even Lavos's real body anyways.
In League of Legends, we have Kassadin and Malzahar. Both have been touched by the Void, an extradimensional space where Lovecraftian creatures lurk. Both wield Void magics, but with very different goals. Whether anything human actually remains of them is debatable.
The GMan of Half-Life... Maybe. To be certain, he's dead center in the unnerving category, has scarily thorough, though unknown amounts of knowledge of the protagonist and events, and displays powers that are magnitudes beyond anything else in the series (it required the entire Vortigaunt race working together just to stall him, and even that didn't last long). And he says he reports to a higher power. There's a good reason a lot of fans compare him to Nyarlathotep.
As of Sengoku Basara 3, Oichi is, if not one outright, at least on her way to becoming one. She's been robbed of the last shred of her sanity, seeing the world through a bizarre, alien dream logic, and is simultaneously the master and puppet of the dark powers she showed in the previous game. She gets better in some of her endings.
Deadly Premonition has Forrest Kaysen, who is revealed to be a dimension-warping abomination. He certainly isn't as indestructible as the average Humanoid Abomination though, as Francis Zach Morgan is able to dismissively murder the son of a bitch with a well placed bullet to the brain.
According to Word of GodWillie is Kaysen's overseer, delivering his instructions from the Red World.
The Outer Space Beings from the Sin and Punishment series are from outside the universe as we know it, have strange and immense powers, have blood that can grant people special powers, are implied to be the source of many of the bizarre lifeforms found in the series... and can look perfectly human. The fluff reveals they can look like anything they want. And Achi, Big Bad of the first game, shapeshifts into a planet for the final boss fight.
Minecraft has the "Enderman" mob, which is based off of Slender Man. They're three-meter-tall, completely black humanoids with glowing eyes. They wander around at night, and unlike other monsters that actively search for you, Endermen ignore you as long as you ignore them. However, if you look directly at them, they turn to stare at you, then attack as soon as you break your gaze. They can teleport to get closer to you, and to dodge arrows. They run quickly at you when you can't see them. When you look back at them, they stop moving and stare at you, with their mouths opening and shaking violently. They're the only mob able to pick up blocks. In a recent update, they've gained a few extra sounds they can make, including a long, rising, unearthly growl that seems to come from nowhere in particular. It was eventually revealed that they're aliens from another dimension called The End, and you need to travel to their homeworld to beat the game (insofar as you can ever "win" a Wide Open Sandbox with no plot).
Dishonored has the Outsider, an...entity that seems to have existed throughout the whole of recorded history - and before. You'd mistake him for a handsome young man in plain clothing were it not for his totally black eyeballs, his tendency to be wreathed in shadow, and that he seems to enjoy hovering a foot or so off the ground. His hobbies include speaking with polite bemusement about mortal affairs, entering people's dreams to inspire bizarre inventions, branding those he deems "interesting" with his mark to grant them really weird powers, being alternately worshipped as a god and vilified as a Satanic figure, and hanging out in a realm called The Void which may or may not be slowly consuming reality as its inhabitants know it. Anecdotal evidence suggests that he may be using A Form You Are Comfortable With, and he's actually a Space Whale...which in the Dishonored universe, means he's pretty Lovecraftian in his appearance (though far from Go Mad from the Revelation levels).
OFF, depending on the Alternate Ending you pick. It helps that the thing's on the very edge between this and a full-blown eldritch in appearance, and that from your perspective, it had you fooled the entire time.
Dark Samus, the main antagonist of the Metroid Prime trilogy, resembles a black, biomechanical version of Samus Aran. "She" began as the titular Metroid Prime, a Metroid mutated by prolonged exposure to Phazon and prophesied by the Chozo as the Worm. Following Metroid Prime's defeat at the hands of Samus, it merged with her Phazon Suit and came back as a twisted doppelganger bent on spreading Phazon throughout the universe and even other dimensions, and was unkillable as long as Phazon existed.
Amnesia: The Dark Descent: The Big Bad, Baron Alexander von Brennenburg, is eventually revealed to be a being from another universe that got exiled into our own. He takes a human form to fit in with our society, but as the game goes on it's clear he is something else. Looking at a portrait of him while low on sanity transforms his face into a horrific corpse-like visage, which is believed by some to be a glimpse at his true form.
Subtly implied with Gardevoir in the Pokémon series. Despite looking, well, human-like, it's not in the "human-like" breeding group. It is in fact in the "Amorphous" group, which means it can breed with things like Weezingnote the living incarnation of Deadly Gas, Muknote a walking pile of toxic sludge, most Ghost types, and a giant electric lampreynote Eelektross. It's the only thing in its egg group that really looks like it doesn't belong there. And in Pokémon X and Y it's now Psychic/Fairy-type, which only adds to this.
Flemeth, the Witch of the Wilds from Dragon Age. It's not yet clear what she is, but she unnerves everybody. Her own daughter Morrigan eventually discovers that Flemeth is no mere demon-possessed mage or Blood Mage, but something worse. Fenris claims that he's met demons, blood mages, and abominations, but he can tell that Flemeth isn't any of those things. Even Justice, a Fade Spirit, has no idea what she is. The only thing certain about her is that she is dangerous. Very dangerous.
Tsukihime has Nero Chaos, who has a body composed of hundreds of animals that can detach from him to attack and feed. Even his mind is a gestalt, and his original personality is slowly being subsumed into the collective consciousness.
Rithuly from Sluggy Freelance, a vaguely defined "dark god" with strong Eldritch Abomination vibes: his "true form is of a great flying Stygian dragon" but he "usually appears man-sized, either as a wispy tentacle-headed dark ghost or a charming handsome man in a white robe adorned with jewelry."
Gunnerkrigg Court: A look into her past reveals that Jones qualifies. Her existence predates life on Earth by at least a few billion years, but she has always looked the same. She has a perfect memory for every instant of her entire history, scratches diamonds, and is impenetrable to x-rays. She claims to lack emotions or imagination; though Antimony has her doubts on this matter, it might just be projection on her (and the readership's) part. Oh, and she has no idea what she is, either. MYSTERY SOLVED!
The Slender Man, pictured above. You can just about mistake him for a human being at a distance (unless he's in full-on Combat Tentacles mode), but come any closer and you start to... noticethings. Marble Hornets, one of the most famous Slendy stories, is an excellent portrayal of this trope. The Slender Man distorts reality just by existing, driving some characters into homicidal madness. He seems to have a goal of some sort, but whatever it is, it's utterly inscrutable.
Another well-known creepypasta creation, The Rake, also counts. A freakish hairless dog-man who seems to have similar stalking habits to Slenderman, albeit being more direct with his victimsnote Slendy watches from a distance; the Rake likes to sit on your bed. While you're in it. Has even showed up in Everyman HYBRID, integrating it into the above mythos.
The SCP Foundation has absolutely every type of abomination, and these are no exception. There's some serious creepyReality Warpers hanging around there.
Dr. Clef claims to be one himself: he discovered what he was at an early age when an idle thought caused the Challenger disaster. He then devoted his life to putting the kibosh on those more selfishly inclined than he. This is still Clef, though, so take it with a mine of salt.
Creepy Child SCP-053 looks and acts like an ordinary three year old girl. She's not. Let's put it this way: SCP-682, an alien reptillian Omnicidal Maniac that hates everything in this universe on principle, likes SCP-053, and the feeling is mutual — once SCP-053 got past her initial fear of the giant terrifying reptiloid. (It's kind of adorable, actually.)
SCP-106 is an entity that resembles a decomposing old man that corrodes everything it touches and has its own Pocket Dimension that it lords over.
SCP-096 is a tall skinny being with disproportionately long arms and enters an Unstoppable Rage and screams like a human when someone looks at its face, regardless of how indirect the method is, and will proceed to kill and [DATA EXPUNGED] that person leaving no trace of them.
Along the lines of the Slender Man, SCP-582 appears and acts out his part in any stories written about him.
Sara Waite, codename Carmilla. She looks like a goddess of lust. Her father's mother is actually Shub-Niggurath. Her mother's ancestry is even creepier.
Tennyo is somehow related to some Eldritch Abomination that was created to eat/destroy the Eldritch Abominations of the Cthulhu Mythos, something that would look at Cthulu and think "ooh, an appetizer!"
Ace in Ruby Quest, a silent, masked Implacable Man who appears to be central to the mysteries surrounding the facility and may or may not be The Worm That Walks. Additionally, all of the normal people in the facility are either on their way here or past it and heading towards pure, concentrated Body Horror.
Atop the Fourth Wall: The Entity/Missingno can apparently only manifest itself in the physical realm by taking the form of another.
Breach qualifies. She's a Creepy Child with extra arms, one set oversized, and creates portals. She keeps people as playthings in her pocket dimension.
Miss Bitters from Invader Zim. Nobody is exactly sure what she is, but human is not on the list of options. She is implied to be older than the Skool (they couldn't make her move so they built it around her and made her a teacher) and has taught at least two generations worth of students. The official website mentions rumors that she is the spawn of an English teacher and a really big snake. Her flashbacks in the series indicate she was once much happier...
Wall-Mart in the South Park episode "Something Wall-Mart This Way Comes". Wall-Mart is actually portrayed as a complete Eldritch Abomination in the episode, being an abstract entity from beyond that exists as long as there is consumerism and poisons every town in which it manifests itself. Near the end of the episode however, it temporarily takes on human form so it can talk to Stan and Kyle.